The direct targets of CBFs: In cold stress response and beyond

Abstract

Cold acclimation in Arabidopsis thaliana triggers a significant transcriptional reprogramming altering the expression patterns of thousands of coldresponsive (COR) genes. Essential to this process is the C-repeat binding factor (CBF)-dependent pathway, involving the activity of AP2/ERF (APETALA2/ethylene-responsive factor)-type CBF transcription factors required for plant cold acclimation. In this study, we performed chromatin immunoprecipitation assays followed by deep sequencing (ChIP-seq) to determine the genomewide binding sites of the CBF transcription factors. Cold-induced CBF proteins specifically bind to the conserved C-repeat (CRT)/dehydrationresponsive elements (CRT/DRE; G/ACCGAC) of their target genes. A Gene Ontology enrichment analysis showed that 1,012 genes are targeted by all three CBFs. Combined with a transcriptional analysis of the cbf1,2,3 triple mutant, we define 146 CBF regulons as direct CBF targets. In addition, the CBF-target genes are significantly enriched in functions associated with hormone, light, and circadian rhythm signaling, suggesting that the CBFs act as key integrators of endogenous and external environmental cues. Our findings not only define the genome-wide binding patterns of the CBFs during the early cold response, but also provide insights into the role of the CBFs in regulating multiple biological processes of plants.

Dehydration-Responsive Element Binding Protein 1C, 1E, and 1G Promote Stress Tolerance to Chilling, Heat, Drought, and Salt in Rice

“…As transcriptional factors, OsDREB1 proteins are expected to bind to specific cis-element motifs in the promoter region of their target genes and affect their gene expression. Because AtDREB1s mainly function as transcriptional activators ( Song et al, 2021 ), we searched among genes with reduced expression in the dreb1ceg mutant compared to the WT for potential direct regulatory targets of OsDREB1C/E/G by the criterion of having DRE/CRT element(s) in their promoter region. We first examined the genes under GO terms uniquely enriched in the mutant but not the WT for chilling down regulated DEGs.…”

“…A total of 53 potential OsDREB1C/E/G target genes based on the features that they contain the DRE/CRT element in the promoter region and that they have a lower expression in the dreb1ceg mutant compared to the WT at 0, 4, or 24 h of chilling treatment. This is likely a stringent criterion because some of the direct target genes of Arabidopsis DREB1 proteins do not have a DRE/CRT element in their promoters ( Song et al, 2021 ). Therefore, more genes could be direct regulatory targets of OsDREB1C/E/G proteins.…”

“…The three Arabidopsis CBF/DREB1 proteins are predicted to positively regulate expression of a total of 346 and 112 COR genes in two independent studies ( Jia et al, 2016 ; Zhao et al, 2016 ). Recently, 146 Arabidopsis genes are defined as direct CBF/DREB1 targets by chromatin immunoprecipitation (ChIP) combined with a transcriptional analysis, and these genes are involved in abiotic stress responses, hormone signaling, and environmental signaling ( Song et al, 2021 ).…”

HbSnRK2.6 Functions in ABA-Regulated Cold Stress Response by Promoting HbICE2 Transcriptional Activity in Hevea brasiliensis

“…We have also noticed that cold stress-induced MDA accumulation in the wild-type plant could be significantly repressed by the overexpression of HbSnRK2.6A or HbSnRK2.6B , suggesting another role of HbSnRK2.6 in plant cold stress tolerance through regulating the expression of reactive oxygen species (ROS)-metabolizing enzymes directly or indirectly. Recently, a large number of AtCBFs downstream target genes were identified in Arabidopsis [ 65 ], shedding a light on whether and how HbSnRK2.6-ICE2 module functions in the maintenance of ROS homeostasis by targeting the genes encoding ROS-scavenging enzymes.…”

Genetic Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.)

“…The protective substances such as osmolytes and cryoprotective proteins accumulate to facilitate cold acclimation and freezing tolerance [ 1 , 6 ]. CBFs are known to bind to the C-REPEAT/DEHYDRATION RESPONSIVE ELEMENT (CRT/DRE) sequence (TACCGCAT) in the promoters of COR genes for their transcription activation in response to cold stress [ 48 , 49 ]. The expression of ABA-dependent COR genes ( Wrab15/17/18/19 ) and ABA-independent COR genes ( WCS19 , WCS120 , Wcor14 , and Wcor15 ) are significantly increased by cold stress in wheat ( Figure 1 ) [ 50 ].…”